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weir12 / DENA

Deep learning model used to detect RNA m6a with read level based on the Nanopore direct RNA data.
MIT License
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LSTM_extract.py predict output nothing #11

Closed William-chen777 closed 2 years ago

William-chen777 commented 2 years ago

Dear professor: when i use the commond: python ./DENA-release/step4_predict/LSTM_extract.py predict --fast5 ./singleFast5/ --corr_grp RawGenomeCorrected_000 --bam ./col.sorted.bam --sites ../candidate_predict_pos.txt --label col --windows 2 2 --processes 20

I get some tmp files, but 3_tmp has nothing. 625867 0_tmp 709963 10_tmp 678042 11_tmp 73825 12_tmp 701523 14_tmp 682437 15_tmp 691647 17_tmp 663647 18_tmp 651893 1_tmp 0 3_tmp 559607 4_tmp 612549 5_tmp 757275 6_tmp 706120 7_tmp 151 8_tmp 522064 9_tmp

And this causes the process to go to sleep. 415378 ? S 0:00 python

What can I do for this problem?

Best wishes.

defendant602 commented 2 years ago

I have encontered the same problem, the command hangs after outputing some tmp files.

python3 LSTM_extract.py predict --processes 10 --fast5 fast5_pass_single --corr_grp RawGenomeCorrected_000 --bam basecalls.bam --sites candidate_predict_pos.txt --label sample --windows 2 2
weir12 commented 2 years ago

Hi, You can safely terminate these processes (including sub-processes), after confirming that the progress bar has reached 100% (add the "--debug" option to activate the progress bar) Liang Ou